Multi-region Sampling Research Articles

NIMG-87. MULTIREGIONAL, MRI-LOCALIZED SAMPLING OF HIGH GRADE GLIOMAS REVEAL SEX-DISTINCT PATTERNS OF 5-ALA FLUORESCENCE AND IMAGING FEATURES

Abstract High grade gliomas (HGGs) are aggressive brain tumors that are difficult to remove completely, leading to poor survival rates. Contrast enhancement on T1Gd magnetic resonance imaging (MRI) has traditionally been used to guide resection, however it often underestimates true tumor burden, adding a layer of uncertainty for surgeons during pre-operative planning. Fluorescence guided surgery using 5-aminolevulinic acid (5-ALA) has emerged as an intraoperative solution and understanding it in conjunction with MRI features can address the limitations of routine T1Gd imaging during surgical planning. Here we investigate sex-specific patterns in HGGs using 5-ALA fluorescence and imaging features. We analyzed a patient dataset of 202 multiregional MRI-localized biopsies from 42 HGG patients (20 male and 22 female). Data included patient demographics, 5-ALA status (positive or negative), MRI annotations (CE = contrast enhancement, NE = non-enhancement, BAT = brain around tumor non-enhancement), and survival outcomes. Statistical analyses included Wilcoxon rank-sum tests, Kruskal-Wallis tests, and chi-squared tests to assess differences in imaging annotations and 5-ALA positive vs negative status among sex cohorts. Among all samples, CE and BAT were associated with higher 5-ALA positivity, while NE was associated with higher 5-ALA negativity (p = 0.02119). Female patients were less likely to have detectable 5-ALA in their multiregional biopsy samples than males (p < 0.0001). CE at the biopsy location was more likely to be indicative of 5-ALA positivity in males than females (p = 0.001927); whereas NE was associated with higher 5-ALA negativity in females than males (p = 0.03426). BAT was associated with higher 5-ALA positivity in males than females (p = 0.03895). Our study reveals sex-specific patterns in 5-ALA fluorescence and image features among HGG patients. These unique features may serve as potential pre-surgical markers for tumor regions that are more likely to benefit from 5-ALA-guided resection.

TMET-02. CELL-INTRINSIC METABOLIC PHENOTYPES IDENTIFIED IN GLIOBLASTOMA PATIENTS USING MASS SPECTROMETRY IMAGING OF 13C-LABELED GLUCOSE METABOLISM

Abstract Glioblastoma (GB) is an inherently heterogeneous and invasive primary brain cancer. Genomic and transcriptomic studies have attempted to classify GB into subtypes that predict survival and that have different therapeutic vulnerabilities. An outstanding question and technical challenge is to visualize the metabolism of a tumour within its native microenvironment and understand to what extent its metabolism is driven by the microenvironment. Patients with GB tumours were infused with [U-13C]glucose and intra-operative multi-regional tumour samples were rapidly snap frozen for analysis using mass spectrometry imaging (MSI). Tissue microenvironment was assessed using multiplexed antibodies in immunocytochemistry (IMC) of contiguous sections. Isotope tracking in human-derived neurospheres and patient-derived xenografts were used to confirm the presence of metabolic phenotypes detected in the human samples and to test the susceptibility of each phenotype to a panel of drugs targeting cellular metabolism. Three metabolic signatures were identified in patient tumours: glycolytic, oxidative and a mixed glycolytic/oxidative phenotype. The phenotypes did not correlate with microenvironmental features, including proliferation rate, immune cell infiltration, and vascularisation. The phenotypes were retained when patient-derived cells were grown in vitro, or as orthotopically implanted xenografts, and were robust to changes in oxygen concentration, demonstrating their cell intrinsic nature. The spatial extent of the regions occupied by cells displaying these distinct metabolic phenotypes are large enough to be detected using clinically applicable metabolic imaging techniques. The phenotypes also demonstrate differential drug sensitivities, suggesting imaging of these phenotypes may be used to stratify patients for personalised therapy trials. This is the first report to demonstrate high resolution imaging of metabolic fluxes in a human tumour in vivo and the presence of different metabolic phenotypes within GB that are tumour cell intrinsic and largely independent of the tumour microenvironment.

NIMG-62. SEX-DISTINCT TRANSCRIPTOMIC SIGNATURES UNDERLY MRI-DEFINED EDEMA PATTERNS IN HUMAN GLIOMAS

Abstract Magnetic resonance imaging (MRI) is key to clinically managing brain tumor patients, however connecting the biology to imaging remains challenging. We previously developed a two-compartment model of MRI signal intensity to quantitatively estimate relative edema abundance from T2-weighted MRIs. Using this model, we previously identified the fatty acid metabolism (FAM) and oxidative phosphorylation (OxPhos) pathways as sex-distinct, with both pathways amplified for high edema in males and low edema in females. The purpose of this project was to further delineate sex-distinct biology associated with MRI-estimated brain tumor edema abundance. We analyzed 179 multiregional samples (Female: 75; Male: 104) from 55 high grade glioma patients (Female: 21; Male: 34) for bulk RNA-Seq. Patients’ pre-surgical multiparametric MRIs were preprocessed and segmented for abnormal regions and normal tissue. Utilizing the segmentations and preprocessed images we estimated the relative fractions of extracellular and intracellular space based on the edema mathematical model. Samples were characterized by their edema scores, which were analyzed using differential expression for high and low edema, gene set enrichment analysis (GSEA) using MSigDB hallmarks, and leading edge interpretation. Based on transcriptomic leading edge analyses of high and low edema samples from sex-separated cohorts, we identified common and sex-distinct enrichment of the FAM and OxPhos pathways underlying edema patterns. Of the OxPhos pathway leading edge genes, 45 were common, 36 were unique to females, and 66 were unique to males. Of the FAM pathway leading edge genes, 8 were common, 39 were unique to females, and 29 were unique to males. Notably, expression of both IDH1 and IDH2 were increased for males in regions of high edema in the OxPhos pathway. IDH3a was decreased for females in regions of low edema in the OxPhos pathway. These data suggest that there may be sex-distinct metabolism underlying MRI measurable edema formation.

Radiological, clinical, and molecular analyses reveal distinct subtypes of butterfly glioblastomas affecting the prognosis

Abstract Background Glioblastoma (GB) is known for its highly invasive nature. Images of butterfly GB (bGB) often illustrate this characteristic, but the molecular background and origins of bGB remain unknown. Methods We analyzed a cohort of 34 bGB patients from our dataset (K-cohort) and 46 bGB patients from publicly available datasets, including TCGA-GBM, CPTAC-GBM, IvyGAP, and UPENN-GBM. Results In the K-cohort, the median age was 66 years, and molecular analyses revealed TERT promoter mutations in 55.9% of cases, with no cases exhibiting H3F3A, HIST1H3B, or BRAF mutations. Sequential radiological imaging from the K-cohort provided unique insights, showing one case originating in the corpus callosum (CC) and three cases originating in the cerebral hemisphere before developing into bGB. Multi-regional sampling supported a mutational trajectory from the hemisphere to the CC. These observations indicate the presence of two distinct radiological origins for bGB. Consequently, we classified cases into CC-type and Hemispheric-type based on the tumor volume ratio within the CC. This subgrouping was clinically meaningful; the CC-type is an independent poor prognostic factor for overall survival, with a hazard ratio of 1.8 (95% confidence interval 1.1-3.0, P = 0.033), and is molecularly distinct by a higher frequency of methylated MGMTp (P = 0.0039) compared to the Hemispheric-type. Conclusions Our results highlight that the radiological features of bGB are not homogenous and can indicate two potential subtypes based on their origins. Further studies are mandatory, but CC-type and Hemispheric-type exhibit distinct clinical backgrounds, outcomes, and molecular features.

CELL-INTRINSIC METABOLIC PHENOTYPES IDENTIfiED IN GLIOBLASTOMA PATIENTS USING MASS SPECTROMETRY IMAGING OF 13C-LABELED GLUCOSE METABOLISM

Abstract AIMS Glioblastoma (GB) is an inherently heterogenous and invasive primary brain tumour. Genetic and transcriptomic studies have attempted to classify GB into subtypes that can identify therapeutic vulnerabilities and predict survival. An outstanding question and technical challenge is to visualise the metabolism of a tumour within its native microenvironment and understand to what extent its metabolism is driven by the microenvironment. METHOD Patients with GB tumours were infused with [U-13C]glucose and intra-operative multi-regional tumour samples were rapidly snap frozen for metabolic tracing analysis using mass spectrometry imaging (MSI). Tissue microenvironment was assessed using multiplexing of antibodies on immunocytochemistry (IMC) of parallel sections. Isotope tracing in human derived neurospheres and patient derived xenografts were used to confirm the presence of metabolic phenotypes detected in the human samples and to test susceptibility of each phenotype to a panel of drugs targeting cellular metabolism. RESULTS Three metabolic signatures were identified in patient GB tumours: glycolytic, oxidative and a mixed glycolytic/oxidative phenotype. The phenotypes did not correlate with microenvironmental features, including proliferation rate, immune cell infiltration, and vascularisation. The phenotypes were retained when patient derived cells were grown in vitro, or as orthotopically implanted xenografts, and were robust to changes in oxygen concentration, demonstrating their cell intrinsic nature. The spatial extent of the regions occupied by cells displaying these distinct metabolic phenotypes are large enough to be detected using clinically applicable metabolic imaging techniques. The phenotypes also demonstrate differential drug sensitivities. CONCLUSION This is the first report to demonstrate high resolution imaging of metabolic fluxes in a human tumour in vivo. In conjunction with studies on patient-derived neurospheres and orthotopically implanted xenografts we have demonstrated the presence of different metabolic phenotypes within GB that are tumour cell intrinsic and largely independent of the tumour microenvironment. These can be imaged clinically and used to stratify patients for personalised therapy.

A unique interplay of access and selection shapes peritoneal metastasis evolution in colorectal cancer.

Whether metastasis in humans can be accomplished by most primary tumor cells or requires the evolution of a specialized trait remains an open question. To evaluate whether metastases are founded by non-random subsets of primary tumor lineages requires extensive, difficult-to-implement sampling. We have realized an unusually dense multi-region sampling scheme in a cohort of 26 colorectal cancer patients with peritoneal metastases, reconstructing the evolutionary history of on average 28.8 tissue samples per patient with a microsatellite-based fingerprinting assay. To assess metastatic randomness, we evaluate inter- and intra-metastatic heterogeneity relative to the primary tumor and find that peritoneal metastases are more heterogeneous than liver metastases but less diverse than locoregional metastases. Metachronous peritoneal metastases exposed to systemic chemotherapy show significantly higher inter-lesion diversity than synchronous, untreated metastases. Projection of peritoneal metastasis origins onto a spatial map of the primary tumor reveals that they often originate at the deep-invading edge, in contrast to liver and lymph node metastases which exhibit no such preference. Furthermore, peritoneal metastases typically do not share a common subclonal origin with distant metastases in more remote organs. Synthesizing these insights into an evolutionary portrait of peritoneal metastases, we conclude that the peritoneal-metastatic process imposes milder selective pressures onto disseminating cancer cells than the liver-metastatic process. Peritoneal metastases' unique evolutionary features have potential implications for staging and treatment.

Abstract B080: A porcine model of pancreatic ductal adenocarcinoma for human scale translational cancer research

Abstract Pancreatic ductal adenocarcinoma (PDAC) remains a highly fatal form of cancer, requiring urgent advancements in diagnostic and therapeutic strategies. Although PDAC mouse models have been crucial in advancing our comprehension of the disease, they present some limitations in replicating key human PDAC aspects. In this study, we present the development of the first large animal model of pancreatic cancer via Cre activatable mutations in the endogenous KRAS and TP53 genes 1,2. In order to activate these mutations in the pancreas, two Cre driver pig lines expressing Cre recombinase from PTF1A 3 and PDX1 were created. Crossing both Cre lines with pigs carrying latent KRAS G12D and TP53 R167H alleles produced double (KC) and triple (KPC) genetically modified animals. Pathological analyses revealed the presence of inter- and intralobular fibrosis with multifocal acinar-to-ductal metaplasia (ADM), some low-grade PanINs, dysplasia, inflammation and duct obstruction in most of the KPC pigs between 3 to 6 months of age. Interestingly, the majority of these pigs already exhibited local metastasis in the lymph nodes, suggesting that the metastatic potential is established early in the tumorigenic process. Age-matched KC pigs exhibited mainly ADM with dysplasia. Flow cytometry and RNA expression analyses of the established pancreatic tumour primary cells revealed a pronounced epithelial-to-mesenchymal transition (EMT). Moreover, both bulk tumour samples and primary tumour cells showed high expression of the pancreatic cancer stem cell marker CD44, with differential expression of its isoforms, including the major isoform and variants 6 and 9. In addition, histological and molecular analyses revealed notable similarities between pig and human PDAC, including molecular subtypes, neuronal invasion and loss of acinar identity. These findings highlight the unique advantage of the pig PDAC model, that allows longitudinal and multi-regional tumour sampling in the absence of any therapeutic interventions. This makes it a valuable tool for developing new diagnostic and therapeutic approaches that can greatly improve patient outcomes in the long run.

Tumour heterogeneity and evolution in advanced thyroid cancer through multiregion and longitudinal sampling

Tumour heterogeneity and evolution in advanced thyroid cancer through multiregion and longitudinal sampling

75 WIRE: Window of Opportunity Clinical Trials Platform for Evaluation of Novel Treatments Strategies in Renal Cell Cancer

Abstract Background Despite the success of immunotherapy and VEGFR directed tyrosine kinase inhibitors (TKIs) for the treatment of renal cell carcinoma (RCC), a significant proportion of patients display primary or secondary resistance to systemic therapy. New treatment approaches are needed for these patients. Pre-surgical clinical trials allow us to study the effects of cancer treatment on the tumour microenvironment, comparing baseline biopsy with post-treatment nephrectomy in a ‘window of opportunity’ study. The results may give us insight into the mechanisms of new cancer therapies, that may be advanced into further clinical trials. Methods The WIRE trial (NCT03741426) is a phase II, multi-centre, multi-arm, non-randomised, neoadjuvant clinical trial platform. The overall aim of the trial is proof of mechanism for new RCC therapies. There are five investigational arms: 1. Cediranib (a VEGFR directed TKI), 2. Cediranib + Olaparib (a PARP inhibitor), 3. Olaparib, 4. Volrustomig (anti PD-1/CTLA-4 bispecific) and 5. Rilvegostomig (anti PD-1/TIGIT bispecific). The study uses a Bayesian adaptive design to optimise recruitment, with pre-specified criteria assessed at interim analyses to stop for futility, continue recruitment to that arm, or move to the next investigational arm. Eligible patients have cT1b+, cN0/1, cM0/1 clear cell RCC, planning to undergo surgery, without medical contraindication to trial therapy. Patients undergo baseline biopsy to confirm clear cell RCC and multiparametric dynamic contrast enhanced (DCE) MRI scan of the primary tumour. For tablet arms 1-3, patients receive at least 14 days of investigational medicinal product (IMP). For immunotherapy arms 4 & 5, patients receive one infusion of IMP. The tumour is re-evaluated by DCE-MRI immediately before surgery. At nephrectomy, multi-region tissue sampling from the tumour is performed both pre-arterial ligation and post resection. Serial translational blood and urine samples are collected before, during and after treatment. The primary endpoint for arms 1-3 is a ≥30% reduction in DCE-MRI assessed capillary permeability (Ktrans) compared to baseline. The primary endpoint for arms 4 & 5 is a ≥30% increase in IHC assessed CD8+ T cell density comparing the resected tumour to baseline biopsy. Secondary endpoints include RECIST v1.1 primary tumour response and adverse events. A comprehensive translational science programme accompanies the trial, which will assess the tumour microenvironment and peripheral blood response to therapy, using techniques including imaging mass cytometry and single cell RNA sequencing. This will allow us to gain a deep understanding of mechanisms of response in each investigational arm. To date, arms 1 & 2 have completed recruitment, and arm 3 is actively recruiting. Conclusions WIRE offers a unique opportunity to investigate the mechanisms of new therapies for RCC. Successful completion of these peri-surgical studies depends on co-ordination between many specialties, including surgery, oncology, radiology, and pathology. The adaptive design allows for efficient allocation of patients to treatment arms to generate optimal data for each IMP. WIRE may identify novel biomarkers of response and toxicity, to inform treatment selection for patients. The data generated will be a foundation for further trials of these IMPs in advanced disease.

HGG-47. SPATIAL SINGLE-CELL PROTEOMIC ANALYSIS MAPS THE DISTINCT PEDIATRIC-TYPE DIFFUSE HIGH-GRADE GLIOMA TUMOR ENTITIES AND DEFINES THEIR TUMOR AND IMMUNE MICROENVIRONMENTS

Abstract Paediatric-type diffuse high-grade gliomas (pDHGG) are a group of molecularly and clinically defined tumor entities of the central nervous system. The investigation of the spatial organization of pDHGG tissues may provide new insights to decipher their heterogeneous nature and identify vulnerabilities in their aggressive behaviour. Here we exploit Imaging Mass Cytometry (IMC), a spatial biology approach enabling multiplex tissue phenotyping at single-cell resolution. We used 16 total formalin-fixed paraffin-embedded (FFPE) tissues from 4 patients including 1 Diffuse hemispheric glioma H3G34-mutant (DHG-H3G34), 1 Diffuse pediatric-type high-grade glioma H3-wildtype and IDH-wildtype (DHGG-WT) and 2 Diffuse midline glioma H3K27-altered (DMG-H3K27, 1 H3.3K27M and 1 H3.1K27M). Classical pathology assessment and DNA methylation profile were also performed. For IMC staining, 2 metal-tag custom-designed antibody panels (tumour and immune) of 31 antibodies were used. The panels include antibodies for differentiated and stem-cell markers, extracellular matrices, immune markers and H3K27M and H3.3G34R variants. An IMC analysis pipeline was developed: images are extracted in tiff format from the proprietary MCD files produced by Hyperion instrument, filtered to remove hot pixels via top-hat and OpenCV in Python, segmented using steinbock and analysed using the IMC Data Analysis toolbox in R, using docker. A total of 209 mm2 of tissue were analysed. IMC analysis showed that DHG-H3G34 displays a higher heterogeneity in terms of cell phenotypes compared to the other tumor entities. Moreover, immune infiltrate of T, B cells, NK and monocytes was observed in the DHG-H3G34 and DHGG-WT tissues, while the DMG-H3K27 had low/no immune infiltrate with the H3.3K27M showing higher PDL-1 expression. Analysis of longitudinal and multi-region samples highlighted trajectories of tumor evolution and identification of extracellular matrix niches in tumor core versus the infiltrative front. Our study provides novel insights into pDHGG complex biology by investigating their tissue architecture, spatial organization and cell-cell interactions.

DIPG-86. INVESTIGATING THE TUMOR ENVIRONMENT AND SIGNALING DEPENDENCIES DRIVING DIFFUSE MIDLINE GLIOMA TUMOR INITIATION, PROGRESSION, AND RESISTANCE: A COMPREHENSIVE APPROACH LEVERAGING BULK MULTIOMICS DECONVOLUTION AND SINGLE-CELL OMICS VALIDATION

Abstract BACKGROUND Diffuse Midline Glioma (DMG) is a incurable tumor affecting children. Recent genomic investigations have identified a recurrent H3K27M mutation which induces global alterations in histone methylation patterns and DNA methylation. These epigenetic modifications hint at pivotal roles in DMG pathogenesis, yet effective therapeutic strategies remain elusive, with median survival rates stagnant at approximately one year. This shortfall stems from two main factors: 1) Inadequate multiomics studies hindering our understanding of DMG evolution and tumor progression, and 2) Limited comprehension of the tumor microenvironment in DMG. METHODS To elucidate DMG’s clonal evolution, we adopted a comprehensive multi-region sampling approach, acquiring 33 specimens from seven patients. Whole-exome and transcriptome sequencing, alongside DNA methylation profiling, were performed. Additionally, we generated one of the most extensive single-cell multiomics datasets (>300,000 cells from 21 additional samples), with a focus on pre- and post-treatment, and dissemination effects in DMG. RESULTS Our analysis delineated a tumor-promoting microenvironment characterized by hypoxia and pro-inflammatory conditions, nurturing genomic alterations and specialized biological processes such as proliferation and epithelial-mesenchymal transition. Notably, a majority of immune cells exhibited M1-like polarization, bolstering pro-inflammatory programs within the tumor milieu. Subclones within the DMG cohort demonstrated dissemination potential, often exhibiting up-regulation of NOTCH, P53, and WNT beta-catenin signaling pathways. These findings suggest that DMG clones harboring dissemination capabilities outside the pons acquire additional phenotypic features, possibly mediated by epigenetic or transcriptional alterations, contributing to enhanced migratory and aggressive behaviors. CONCLUSIONS Our study unveils the parallel evolution of DMG at genetic, epigenetic, and transcriptional levels, unveiling novel subclonal phenotypes governing tumor behavior. Crucially, we identify critical environmental shifts such as hypoxia and inflammatory changes, coupled with specialized signaling programs, driving dissemination and resistance phenotypes. These insights may pave the way for generating accurate genetically mouse models and targeted therapeutic interventions to combat this challenging malignancy.

Identification of a gene expression signature of vascular invasion and recurrence in stage I lung adenocarcinoma via bulk and spatial transcriptomics.

Microscopic vascular invasion (VI) is predictive of recurrence and benefit from lobectomy in stage I lung adenocarcinoma (LUAD) but is difficult to assess in resection specimens and cannot be accurately predicted prior to surgery. Thus, new biomarkers are needed to identify this aggressive subset of stage I LUAD tumors. To assess molecular and microenvironment features associated with angioinvasive LUAD we profiled 162 resected stage I tumors with and without VI by RNA-seq and explored spatial patterns of gene expression in a subset of 15 samples by high-resolution spatial transcriptomics (stRNA-seq). Despite the small size of invaded blood vessels, we identified a gene expression signature of VI from the bulk RNA-seq discovery cohort (n=103) and found that it was associated with VI foci, desmoplastic stroma, and high-grade patterns in our stRNA-seq data. We observed a stronger association with high-grade patterns from VI+ compared with VI- tumors. Using the discovery cohort, we developed a transcriptomic predictor of VI, that in an independent validation cohort (n=60) was associated with VI (AUROC=0.86; p=5.42×10-6) and predictive of recurrence-free survival (HR=1.98; p=0.024), even in VI- LUAD (HR=2.76; p=0.003). To determine our VI predictor's robustness to intra-tumor heterogeneity we used RNA-seq data from multi-region sampling of stage I LUAD cases in TRACERx, where the predictor scores showed high correlation (R=0.87, p<2.2×10-16) between two randomly sampled regions of the same tumor. Our study suggests that VI-associated gene expression changes are detectable beyond the site of intravasation and can be used to predict the presence of VI. This may enable the prediction of angioinvasive LUAD from biopsy specimens, allowing for more tailored medical and surgical management of stage I LUAD.

Representation of genomic intratumor heterogeneity in multi-region non-small cell lung cancer patient-derived xenograft models

Patient-derived xenograft (PDX) models are widely used in cancer research. To investigate the genomic fidelity of non-small cell lung cancer PDX models, we established 48 PDX models from 22 patients enrolled in the TRACERx study. Multi-region tumor sampling increased successful PDX engraftment and most models were histologically similar to their parent tumor. Whole-exome sequencing enabled comparison of tumors and PDX models and we provide an adapted mouse reference genome for improved removal of NOD scid gamma (NSG) mouse-derived reads from sequencing data. PDX model establishment caused a genomic bottleneck, with models often representing a single tumor subclone. While distinct tumor subclones were represented in independent models from the same tumor, individual PDX models did not fully recapitulate intratumor heterogeneity. On-going genomic evolution in mice contributed modestly to the genomic distance between tumors and PDX models. Our study highlights the importance of considering primary tumor heterogeneity when using PDX models and emphasizes the benefit of comprehensive tumor sampling.

Multiregional transcriptomics identifies congruent consensus subtypes with prognostic value beyond tumor heterogeneity of colorectal cancer

Intra-tumor heterogeneity compromises the clinical value of transcriptomic classifications of colorectal cancer. We investigated the prognostic effect of transcriptomic heterogeneity and the potential for classifications less vulnerable to heterogeneity in a single-hospital series of 1093 tumor samples from 692 patients, including multiregional samples from 98 primary tumors and 35 primary-metastasis sets. We show that intra-tumor heterogeneity of the consensus molecular subtypes (CMS) is frequent and has poor-prognostic associations independently of tumor microenvironment markers. Multiregional transcriptomics uncover cancer cell-intrinsic and low-heterogeneity signals that recapitulate the intrinsic CMSs proposed by single-cell sequencing. Further subclassification identifies congruent CMSs that explain a larger proportion of variation in patient survival than intra-tumor heterogeneity. Plasticity is indicated by discordant intrinsic phenotypes of matched primary and metastatic tumors. We conclude that multiregional sampling reconciles the prognostic power of tumor classifications from single-cell and bulk transcriptomics in the context of intra-tumor heterogeneity, and phenotypic plasticity challenges the reconciliation of primary and metastatic subtypes.

B2B informal networking influences on relational outcomes in emerging and developed nations: a multiregional empirical study

PurposeThis study aims to investigate how indigenous socio-cultural (ISC) practices within informal networks, such as guanxi and wasta, provide benefits beyond mere access. Specifically, the authors explore their global impact on B2B relationships, focusing on reciprocity. A multiregional sample extends research on ISC practices in B2B relationships by examining contingency effects of informal network ties.Design/methodology/approachThe authors surveyed 404 buyers in two developed (Hong Kong and Portugal) and two emerging economies (Kuwait and Colombia), and also categorized by strong and weak informal network ties. Using structural equation modeling, the authors examined a relationship marketing (RM) model from a typology (Clubs, Sociocracies, Clans and Compadres) for assessing contingency effects.FindingsThe study reveals that in developed economies with strong formal institutions, negative aspects of favor reciprocity norms intensify unless informal networks are driven by strict sociomoral obligations. This supports research indicating that contractual governance competes rather than complements relational governance. Moreover, trust-building processes are crucial in regions with low uncertainty tolerance to mitigate adverse effects.Practical implicationsSuppliers from developed nations need more than cultural communication insights when engaging in business in emerging markets. We acknowledge changes buyers may expect adherence to reciprocity rules embedded in the ISC practices of their informal networks.Originality/valueThis study pioneers a typology of social structures to analyze ISC practices across buyers with varying formal institutional strength and informal network ties. It sheds light on institutional dynamics, trust-building processes, and nuances surrounding both positive and negative aspects of reciprocity practices. Furthermore, it broadens the scope of RM to Asia, Europe, Latin America and the Middle East.

Using the pan-genomic framework for the discovery of genomic islands in the haloarchaeon Halorubrum ezzemoulense.

In this study, we use pan-genomics to characterize the genomic variability of the widely dispersed halophilic archaeal species Halorubrum ezzemoulense (Hez). We include a multi-regional sampling of newly sequenced, high-quality draft genomes. The pan-genome graph of the species reveals 50 genomic islands that represent rare accessory genetic capabilities available to members. Most notably, we observe rearrangements that have led to the insertion/recombination/replacement of mutually exclusive genomic islands in equivalent genome positions ("homeocassettes"). These conflicting islands encode for similar functions, but homologs from islands located between the same core genes exhibit high divergence on the amino acid level, while the neighboring core genes are nearly identical. Both islands of a homeocassette often coexist in the same geographic location, suggesting that either island may be beyond the reach of selective sweeps and that these loci of divergence between Hez members are maintained and persist long term. This implies that subsections of the population have different niche preferences and rare metabolic capabilities. After an evaluation of the gene content in the homeocassettes, we speculate that these islands may play a role in the speciation, niche adaptability, and group selection dynamics in Hez. Though homeocassettes are first described in this study, similar replacements and divergence of genes on genomic islands have been previously reported in other Haloarchaea and distantly related Archaea, suggesting that homeocassettes may be a feature in a wide range of organisms outside of Hez.IMPORTANCEThis study catalogs the rare genes discovered in strains of the species Halorubrum ezzemoulense (Hez), an obligate halophilic archaeon, through the perspective of its pan-genome. These rare genes are often found to be arranged on islands that confer metabolic and transport functions and contain genes that have eluded previous studies. The discovery of divergent, but homologous islands occupying equivalent genome positions ("homeocassettes") in different genomes, reveals significant new information on genome evolution in Hez. Homeocassette pairs encode for similar functions, but their dissimilarity and distribution imply high rates of recombination, different specializations, and niche preferences in Hez. The coexistence of both islands of a homeocassette pair in multiple environments demonstrates that both islands are beyond the reach of selective sweeps and that these genome content differences between strains persist long term. The switch between islands through recombination under different environmental conditions may lead to a greater range of niche adaptability in Hez.

Abstract 4249: Establishment and analysis of patient-derived high-grade serous ovarian cancer organoids for disease modeling and drug testing

Abstract Purpose: Ovarian cancer is the most lethal gynecologic cancer. Majority of ovarian cancers belong to the subgroup of high-grade serous ovarian cancer (HGSC). Its standard treatment is surgery and chemotherapy with platinum and taxane-based compounds, for which almost all patients become resistant. We have established a panel of patient derived 3-dimensional (3D) HGSC long-term tumor organoid cultures for personalized disease modeling, drug screening and evaluation of the efficiency of potential new treatments to be used in preclinical research. Methods: Tumor tissues or ascites from &amp;gt; 30 HGSC tumors were set up as long-term 3D organoid cultures (PDOs). RNA and whole genome sequencing was performed from the original tumors and from PDOs. Pluripotency and proliferation were assessed via high-throughput immunofluorescent detection of PAX8 and Ki67. Resistance towards standard treatment and response to additional selected drugs and drug combinations were evaluated in cell death and proliferation assays. Imaging and image-based quantifications were performed under 3D setup. PDOs were set up for in vivo drug testing in immunodeficient NOD/Shi-scid/IL-2Rgnull (NOG) mice. Summary: A set of HGSC PDOs of different longitudinal, prospective, and multiregional samples has been established representing the three evolutionary states of HGSC: evolving, maintaining and adaptive state. They are ready to be used as rational and effective models for studying drug interventions. Supportively, results of preclinical studies with PI3K inhibitor Alpelisib matched the published patient responses. Tumor evolutionary analysis based on data of longitudinal, prospective, and multiregional collected samples suggest further targetable pathways that can mediate chemotherapy resistance and pinpoint potential targets for drug intervention. Conclusion: Inhibition of these pathways with simultaneous targeting of other cellular functions, such as lysosomal-mediated cell death, may be highly effective alternative treatment option. 3D imaging and efficient image analysis are necessary tools to understand tumor organoid biology and drug responses to assist development and pre-clinical evaluation of new treatments. This study is a part of the DECIDER project (https://www.deciderproject.eu/, NCT04846933). Citation Format: Tuula Kallunki, Anna R. Lauridsen, Aikaterini Skorda, Alexandra Lahtinen, Marie L. Bay, Benita Rasmussen, Kaisa Huhtinen, Taru Muranen, Jaana Oikkonen, Johanna Hynninen, Sampsa Hautaniemi. Establishment and analysis of patient-derived high-grade serous ovarian cancer organoids for disease modeling and drug testing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4249.

Abstract 4360: Integrative analysis of multiplex interphase FISH copy number with whole exome sequencing identifies tumor evolution in Stage II colon cancer

Abstract Colon cancer ranks as the second leading cause of cancer-related death worldwide. Although standard therapies are highly effective in stage II lymph-node negative colon cancers, about 10-15% of these patients show disease relapse within the next 5-year period after intended curative surgery. Extensive prior research has highlighted the role of intratumor heterogeneity, arising from genomic instability, as a leading contributor to metastasis in colon cancer. In the current study, we pioneered the integration of Multiplex Interphase FISH (miFISH) and Whole Exome Sequencing (WES) data aiming to depict intratumor heterogeneity and delineate the landscape of genetic aberrations that underlie the early metastatic potential in stage II colon cancer patients. To this aim, we have showcased the genome-wide copy-number alterations and single nucleotide mutations derived from WES analysis of samples obtained from primary stage II colon tumors and their patient-matched liver metastases of nine patients using multi-region sampling. miFISH was employed for the concurrent quantification of copy-numbers for nine genes relevant to colon cancer and a centromeric control probe in intact tumor nuclei derived from archival patient material allowing us to establish ploidy baselines and gain and loss patterns for the genes analyzed. Our study was revealing of several copy number alterations, such as gains of chromosomes 1q, 7, 8q, 13q and 20, and losses affecting chromosomes 17p and 18, which were confirmed by miFISH. Based on our SNV data, most frequently mutated genes were APC, TP53, KRAS. We were able to show several mutations in genes belonging to specific pathways most commonly altered in colorectal cancer, such as APC, TCF7L2, AXIN2, FBXW7 in WNT signaling, SMAD4 in TGF-ß signaling, PIK3CA and PTEN in PI3K signaling and KRAS in RTK-RAS signaling pathways. In nearly all cases, subclones that led to metastasis were already present in the primary cancer, indicating a direct progression from the primary to metastatic disease. However, the divergence from the primary tumor to metastasis enabled us to uncover several potential genetic aberrations present in the metastasis but not observed in the primary tumor. Moreover, in one of our cases, despite harboring APC and TP53 mutations in both the primary and metastatic tumor, unique mutations for these genes along with several distinct mutations in the metastasis were identified. These observations suggest that the metastasis might not be related to the primary tumor analyzed and may have arisen from an independent lesion. In conclusion, applying miFISH and WES to decipher the mutational and copy number landscape in metastatic stage II colon cancer provided comprehensive insights into the complex and heterogenous nature of primary colon cancer and the clonal evolution leading to subsequent liver metastases. Citation Format: Sanam Yaghoubi, Kerstin Heselmeyer-Haddad, Ivan Archilla, Carolina Parra, Darawalee Wangsa, Giancarlo Castellano, Jack Zhu, Diba Yaghoubi, Sara Lahoz, Veronica Pablo-Fontecha3, Daniela Hirsch, Wei-Dong Chen, Thomas Ried, Miriam Cuatrecasas, Paul S. Meltzer, Jordi Camps. Integrative analysis of multiplex interphase FISH copy number with whole exome sequencing identifies tumor evolution in Stage II colon cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4360.

Abstract 6944: Transcriptional programs underpinning reoccurring cancer cell states, plasticity and tumour phylogenies in clear cell kidney cancer

Abstract Intratumor heterogeneity (ITH) is a substrate for tumor evolution and confers amenability to stressors and therapies. Sources of ITH include subclonal mutations, microenvironmental factors, and plasticity whereby a cell has the ability to adopt different cell states. Clear cell kidney cancer (ccRCC) has a well-characterized genetic initiating event - VHL inactivation - resulting in activation of HIF-1 and HIF-2 transcription factors. Although VHL inactivation is consistently clonal in nature, ccRCC nonetheless exhibits extensive genetic and morphological ITH. This makes ccRCC an excellent model in which to study ITH. We performed single cell RNA-seq on multiregional samples from kidney tumors and macroscopically normal kidney tissue. We obtained 55 samples from 16 tumors and used the 10x Genomics platform to obtain gene expression data from ~150,000 single cells, including ~80,000 cancer and normal epithelial cells. We identified three cancer cell states, co-existing in all clear cell kidney cancer tumors analyzed and marked by different gene expression programs: 1) differentiated-like cells marked by proximal tubule cell genes characteristic of the cancer cell of origin; 2) epithelial-mesenchymal transition (EMT)-like cells and 3) injured-like cells. Differentiated markers and EMT markers were associated with good and poor prognosis, respectively, indicating that these cell subpopulations are clinically important. Notably, these cell states are also present in the normal proximal tubule although in different proportions to the tumor samples, which contain more cells in the EMT-like and injured-like states. This suggests that the core features of ITH are inherent to the cell of origin of the cancer, but that the cell state trajectories are dysregulated in the tumor. Furthermore, in tumors these states exist as a continuum, whereby transitional cells in between states appear to exist, suggesting that cancer cells are continually and dynamically transitioning between states. Lastly, we used chromosomal copy number variation (CNV) patterns to study genetic ITH. We examined the effect of 14q loss, which is associated with ccRCC metastasis, on gene expression. We found that 14q loss is associated with downregulation of HIF-1 transcriptional activity together with a reciprocal increase in HIF-2 activity, MYC activity and oxidative phosphorylation, highlighting potential mechanisms by which 14q loss may driver ccRCC metastasis. Citation Format: Olivia Lombardi, Ran Li, Lisa Browning, Faiz Jabbar, Hannah Evans, Peter J. Ratcliffe, David R. Mole. Transcriptional programs underpinning reoccurring cancer cell states, plasticity and tumour phylogenies in clear cell kidney cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6944.

Abstract 1609: Inferring the T cell repertoire dynamics in non-small cell lung cancer metastases

Abstract Non-small cell lung cancer (NSCLC) is a highly complex disease, characterized by extensive genomic heterogeneity and dynamic evolution under therapeutic pressure. This evolution can lead to alterations in the antigens expressed by cancer cells, thereby influencing the T cell repertoire (TCR) as T cells expand in response to foreign antigens. Despite the central role of TCR in cancer progression and treatment response, only few studies have investigated the temporal and spatial changes in the TCR repertoire. In this study, we delve into the role of the TCR repertoire in metastatic progression in NSCLC. We conducted TCR sequencing of multiregion primary tumors, normal-adjacent tissues, and post-mortem metastases sampled from a cohort of 22 patients enrolled in the TRACERx and PEACE studies. Our findings reveal that primary tumor regions and normal-adjacent tissues exhibit similar fractions of expanded clonotypes. However, a higher proportion of expanded intratumoral TCRs were privately expanded in the tumor samples, suggesting a unique TCR landscape within the tumor microenvironment. The TCR repertoire across multiregion primary tumor samples was largely homogenous, with most expanded clonotypes shared across at least two regions. However, only a small fraction of these clonotypes were tracked in metastases, indicating a significant shift in the TCR repertoire during metastatic progression. Notably, the expanded clonotypes that persisted over time from early to late stage disease were significantly enriched for clonotypes ubiquitously expanded in the primary tumor across all regions. This was not shown to be associated with an increased likelihood of generation via VDJ recombination, suggesting a tumor-specific immune response. The expanded TCR repertoire in the postmortem metastases clustered mainly by anatomical site, suggesting an immune response driven by tissue-resident T cells. Moreover, we found a significant positive correlation between repertoire dissimilarity and genomic distance, suggesting that T cell clones track with tumor clones across spatial sites within patients. Our study demonstrates the significant spatiotemporal dynamics of the TCR repertoire during the metastatic progression of NSCLC, orchestrated by both tissue-resident T cells and the genomic evolutionary trajectory of tumors. Such an exploration could provide valuable insights to inform future strategies for immunotherapy treatments and enhance clinical monitoring of patients. Citation Format: Corentin Richard, Sonya Hessey, Cristina Naceur-Lombardelli, Selvaraju Veeriah, Gayathri Nageswaran, Crispin Hiley, Sergio Quezada, Benny Chain, TRACERx and PEACE Consortia, Charles Swanton, Mariam Jamal-Hanjani. Inferring the T cell repertoire dynamics in non-small cell lung cancer metastases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1609.